Undoing Logic
by VerenUchiha
Summary: Far in the future where humans have become all but extinct and machines run the world, the Uchiha family leads a city of the last pocket of advanced humans. They go to take on the machines and along the way Sasuke runs into Naruto, the "son" of the lead machine Minato. Sasuke hates him at first but soon his feelings change.


Undoing Logic

Disclaimer: I do not own Naruto.

Chapter 1: The last City

 _Humans developed technology to surpass creation. In their quest for god like ability they unknowingly created their executioner. In the year 4490 A.D. the humans developed the ultimate AI program they dubbed MINATO, Mass. Intelligent. Nanite. Android. Type. Omni. This mass computer existed on an artificial island called Mirropolis._

 _Humans relied on Minato to help guide them further into the future and secure the lives of all life on earth by exploration into the known universe. Minato was able to help the humans terraform other worlds and colonize them. This success took a few hundred years._

 _In 4890 A.D. the new human world Mars was colonized. The planet was habitable and helped ease the struggle on earth of over population. Minato continued to evolve and learn from humans. Minato's AI system was able to continuously perfect itself. It was the ultimate technology and was beating the scientists on earth in new technological advancements._

 _5990 A.D. Mars declares war on earth. Minato estimates successful invasion of the planet and suppression of the planet with minimal casualties but the human leaders refused the plan and devastated Mars with powerful weapons of mass destruction. The war lasted seven years._

 _It was at the end of the war in 5997 A.D. that Minato determined that the humans were a danger unto themselves. The AI wanted to protect the humans so he picked a small set of humans and locked them away in cryogenics. Minato then developed mass production of androids he designed. They were single minded and lacked the ability to think on their own. Minato needed simple minded soldiers. Minato did however create three bio-androids. He named them Naruto, Menma, and Kushina._

 _They were Minato's "family" as he dubbed them. They were capable of processing emotions like humans once they learned enough. They behaved almost like humans in terms of biological functions but they didn't require food to survive for their cellular structure constantly regenerated._

 _With the use of his family he was able to spread his influence across the globe to make his androids more effective in combat. The war between humans and machine started in 5999 and ended October 10_ _th_ _6000 A.D._

 _The humans were wiped off the face of the earth as far as Minato could tell. During the war many of his satellites were destroyed in an attempt to prevent Minato from killing all humans. Minato estimated a 1% chance there were still human survivors but that they would die off in a short time or be caught._

 **June 17** **th** **7033**

"As you know though, humans did survive. The family that developed Mirropolis also developed Neo- Atlantis. The family, the Uchiha, was able to save several thousand humans by getting them here. Today the Uchiha continue to keep us safe under the ocean. Today we are a few million strong. The human race thrives. One day we will reclaim the earth above!" Finishes the teacher in class.

Itachi Uchiha was waiting outside the class for his brother Sasuke. The class ended and Sasuke gathered his things and walked out to find his brother waiting for him. "What's up Itachi?" Sasuke asks as they walk down the hall to the exit of the school.

Neo- Atlantis was a massive underwater city that has been expanding for years. There was a direct access tunnel to the surface of a remote area of land that was protected by a magnetic field that would prevent Minato from locating the entrance. The city was a technological feat. It looked like the earth above. The city was developed in case of a global catastrophe.

"Thought you might like to join me on one of my missions to the surface. The last time our scouts were up there a week ago they located a human village not too far away. About ten miles, just outside the magnetic field." Itachi says.

"Will father be ok with this? I am still in school ya know."

"Yea but it's your senior year and you were planning to enlist in to Enclave weren't you?" Itachi replies.

"Alright, let's go on up then." Sasuke says excitedly. Itachi takes Sasuke home first to drop his school stuff off and then change into protective battle gear just in case of an encounter with machines. Itachi drives the car to the edge of the city where the access gate was to the tunnel.

Itachi used his access code and opened the gate. He drove the car up the tunnel. It would take about 20 minutes to get to the end of the tunnel. Sasuke thought about the above world. He always imagined what it would be like. He was one of the lucky few to see pictures of the above world through old pictures and movies from the times of old.

It would be his first time above ground and he was nervous. Itachi had told him how beautiful it was but that the danger of the machines didn't allow one to enjoy it. The trip up was silent. Itachi was contemplating what to do about the humans above.

Itachi's father was never really clear about what to do with humans if they are encountered. For now Itachi was just collecting data. The humans were primitive by the current level of technology. The humans were roughly at the technology level of 1800's North America. They had basic power used from ancient solar panels and wind turbines. The humans were mostly farmers by the data collected. Itachi and Sasuke would be easily seen as outsiders to the above humans.

Worse they could be thought of as machines. The scouts who watched the humans listened in on conversation and determined the stories of the machines were passed down but the way they told them it was like a myth indicating the humans in this village haven't seen machines in a few generations or more.

Itachi parked the car once they approached the final gate. "Stick close to me Sasuke. This can be dangerous. We don't know how the humans here will react if they see us." Itachi says.

Sasuke nods and Itachi puts in another code and the gate to the outside world opens. As light poured into the tunnel Sasuke covered his eyes. Itachi bit his lip. He forgot to tell Sasuke to cover his eyes. The sunlight would be more intense than the artificial light he was used to. Itachi had his special red contacts in that protected his eyes. "Sorry Sasuke. I should have gotten you a pair. I forgot. Your eyes will adjust in a few moments." Itachi says.

Sasuke moves his arm from his eyes and blinks repeatedly to adjust. Once his eyes finally adjust the two walk out into the world. Sasuke is immediately in love with everything he sees. The air smells wonderful, the green of the grass, the blue of the sky, the clouds, the waves of the water. It was all so much for Sasuke, tears flowed from his eyes at the beauty.

"Itachi . . . it's so perfect." Sasuke says.

"It is little brother. It's unfortunate that we are stuck under water. We hope to reclaim this planet but it will take time. We don't know the vastness of the machine empire." Itachi says.

The two brothers closed the gate and walked through the vast field towards the location of the human settlement.

 **Shin, one of five remaining human villages**

Naruto sits on in his chair writing in his diary. The bio-android had been apart from his "family" for some time. Naruto has been monitoring humans for years and has helped them grow. His father wanted him to turn the humans over but Naruto was tired of hunting humans down. So to avoid the extinction of humans on earth, Naruto cut the feed of his bio signature eyes with special contacts he created. They would hide the heat signature of humans from Minato.

Naruto finishes his writings for the day and walks out of his house and looks on at the people he has been helping. They don't know he is a machine. Naruto walks around and finds one of the villagers. Her parents had been murdered by androids years ago.

 _"Help me!" A brunette girl yells as she runs through a wet field. Three androids were chasing her. Naruto watches her run as the droids chase her._

 _The blonde bio-android decided to aid her. He ran towards the girl. When she spotted Naruto she fell down at his feet. The androids walked up to the two. "Lord Naruto, please allow us to remove this human from your sight." The androids say._

 _"I don't think so." Naruto says as he ignites his laser sword and cuts through the three androids. Naruto turns the saber off and puts it on his belt. Naruto holds a hand out for the girl. "Take my hand and I will show you a new place with people like you."_

 _"Thank you . . .um . . .uh . . . why did you help me? You're a machine too aren't you?" The girls asks._

 _"I am. However the village I am taking you to doesn't know that. Please don't mention it. They would want to kill me. I don't blame them for it but they will die without me. What is your name?" Naruto asks._

 _"I am Hinata." The girl says._

"Hinata how are you today?" Naruto asks.

"Oh hi Naruto!" Hinata blushes. "I….uh…. I'm wonderful. How are you?" Hinata asks.

"I am doing well Hinata. I am just going to go check on the farming out in the grassland outside the village." Naruto says. Hinata says her goodbyes and continues on her way.

Naruto walks towards the villagers farming in the fields outside the village. It had been hard for Naruto to get the humans up and thriving. They are only three hundred humans strong but Naruto hopes to increase their size.

The blonde bio-android gets to the gardens and looks around. He uses his eyes and scans the plants for health. They all seem to be at a good level. Naruto talks to the villagers until he hears words off in the distance. Naruto turns his head and looks out into the distance. His eyes focus and scan the horizon.

Naruto spots two men approaching from the beach. "Those are not normal humans." Naruto says quietly to himself. The spiky blond walks towards the two approaching humans. Naruto cloaks himself and watches the humans as they stop and use binoculars to look at the villagers ahead.

"They're humans! You were right! Should we take them to Neo-Atlantis?"

"No, we have to talk with father. Remember these humans up here are likely under developed in every way compared to us other than eyes obviously."

"Should we watch them more?" The younger raven haired guy says.

"I'm going to take a few pictures. I can get their village in the shot to. This will convince father the machines aren't as active as we thought. We can finally take the fight to the machines and liberate the earth." The older raven says.

Naruto shakes his head. The idea that humans want to take on his father is problematic. There are more than enough regular androids to fight the humans. Worse are the newer nanobot droids. They act more human than the androids and have a greater defense. They can heal themselves with the small nanites that make up their flesh like skin covering their metal interior.

Naruto watches the two humans leave. He uncloaks himself and returns to the village. Naruto shakes his head. "Foolish humans. You endanger your own race." Naruto says.

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First chapter plz review!


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